The Matrix: Restarted
by sweetheartgrl13
Summary: The machines have made a truce with Zion and saved Neo. But not all the machines agree with the treaty. once again Neo has to save humanity.
1. Chapter 1

**Chapter 0**

After Neo's Fight with Smith the Machines had created a treaty with Zion. They would be in peace as long as both sides kept the treaty. Not every program agreed with the treaty though. Some wanted more power like they had in the Matrix. Some just wanted to see the humans in captivity. The agents hated Zion and still wanted to see its downfall. The Architect wanted to see his world be put to use again. The Merovingian wanted to rule. The programs that wanted to keep the Matrix up and running left and made their own city. With them they brought all the Matrix software and millions of captive humans. The Architect went to work on another Matrix. The Matrix still existed.

**Somewhere in the Matrix…**

Smith opened his eyes. Where was he? The fight! He lost right? No. He was still alive. Smith looked around. He was in a white room with no walls. It never ended. Suddenly the ground turned green. It was grass. A tree was next. Now a building. A playground, cars, benches, stores. Smith realized what was happening. Some one was creating a new Matrix. A person popped up. Smith smirked. He walked over to the confused human.

"Where am I?" Asked the human. Smith brought his arm back and drove it into the human. All that happened was the poor human flew back and hit his head on the ground. He was knocked out immediately. Smith looked at his hand confused. He couldn't clone himself any more. He reached up to his ear. What he felt disgusted him. The earpiece was there, snug tight in his ear.

"Great!" he yelled. He was back where he started.


	2. Chapter 2

Chapter 1

Neo opened his eyes then quickly shut them again. Why was it so bright? Where was he? What happened?

"You better get over here Morpheus. Neo is awake!" Neo attempted to open his eyes and failed. It was just too bright instead he decided to try to remember how he got there.

"It's a miracle!" Neo recognized this voice. It was Morpheus. He went back to his thoughts. Smith. There was a huge fight between them. Smith beat him and cloned him. He remembered the terrible feeling of being cloned. But it didn't stop at that. He somehow was brought back. He beat Smith. But he died there. Didn't he? Maybe this was heaven. But then Morpheus wouldn't be there. So what happened? He couldn't think anymore he was too exhausted to think. He opened his eyes once more to see Morpheus smiling down at him. Wait he could see! Exhaustion set in too quickly for him to do anything else.

**A couple days later…**

Morpheus entered the first aid station for the fifth time in an hour to check on Neo. It still amazed him that the machines had helped him get Neo back. The machines had sent them a message telling them everything and agreeing on a peace treaty. How Neo had gotten his eyesight back was still a mystery to him though. He hoped that Neo could shed some light on that one. Morpheus went through the routine, checking Neo's vitals, making sure everything was okay. So far there hadn't been anything wrong. Hopefully that would keep up. No one had any idea how long Neo would be like this. Morpheus just guessed that he needed some rest.

Morpheus knew that Neo would be extremely happy when he wakes up because Trinity was already awake. She had almost died in the machine city when they crashed their hovercraft. After Neo made peace with the machines, they found her and some how brought her back to life. They escorted both Neo and Trinity back to Zion and helped them with their technology. Trinity, despite what she had gone through, Woke up almost three hours after being brought to Zion. She visited Neo even more than he did. Every one wanted to visit him to pay their thanks but only the crewmembers were allowed to visit Neo.

Morpheus sat down on a chair and settled in for a while. A few minutes later the door to the first aid room opened and Trinity walked in for her visit.

"Hi Morpheus." She said smiling. She walked over to the chairs and sat next to Morpheus.

"Hello Trinity." He said.

"How are you?" She asked casually.

"I've been better." He replied.

"Yeah." She said understanding him completely. Absentmindedly, she glanced over at Neo. Morpheus could see that she needed to be alone for a while so he stood up. Trinity looked up at him.

"I'm going to go check on things." He said smiling.

"Okay." She said, "Thank you." He nodded and turned to leave. At the last second he turned and looked at Trinity.

"Don't worry. He'll wake up soon." He assured. She smiled half-heartedly.

"Yeah." She said quietly. Morpheus turned away and left Trinity with Neo. Trinity stood up and walked over to the table where Neo was peacefully sleeping. Some how it was both calming and disturbing to her. She loved to watch him sleep, so calm. But it always reminded her of when he was in a coma. It hurt her to think about how he had to depend on her when he couldn't see, how he wasn't able to see her before she died once again. The devastated look on his face. She closed her eyes and grabbed his hand. It comforted her to feel his pulse in his hand.

"Your alive?" Said a voice. Trinity looked up and searched for the source of the voice. She felt Neo's hand squeeze her hand a bit. She looked down and saw Neo smiling up at her.

"Oh my god." She whispered.

"What happened?" He asked.

"The machines saved us." She explained.

"Interesting." Said Neo. He sat up slowly and pulled out the IV in his arm. Trinity flung her arms around him.

"I missed you." She whispered.

"I missed you too." He said holding her.

"Why do I always get second chances?" She said tears welling up in her eyes.

"Don't worry." He laughed. "I've died twice too." Trinity hugged Neo harder and hoped she wouldn't ever have to leave again.


	3. Chapter 3

Chapter 2 

Trinity had the nurses alerted about Neo and they did one last check. They made sure that he was healthy and that he wouldn't need any medications. Morpheus was extremely delighted that he had finally woken up. Neo was moved from the first aid room to his own room. Trinity had already moved all his stuff up there so he slept there that night with her in his arms.

"What happened after the crash?" said Trinity catching Neo off guard. He hesitated for a second.

"I did as you told me to and I went on to talk to the machines. At first they didn't even want to listen to me but we eventually came to terms. The agreed to plug me into the matrix to fight Smith and in return they would stop fighting." Neo paused a minute. Trinity waited patiently, wanting to hear his story.

"They plugged me in and when I got there everyone had turned into Smiths." He said starting again, "when we started fighting, he jumped into the air and stayed there. He had somehow gotten the ability to fly. I fought harder than I had ever fought before but he got the upper hand. In the end he cloned me." Neo looked down to see Trinity's eyes wide in horror. He pulled her closer, comforting her.

"The machines somehow revived me and that destroyed all the Smiths. That's all I remember. I don't even know how I have my eyesight back." He said. Trinity let it soak in a bit. It was absolutely amazing that they were both still alive.

"Thank you." She whispered.

"For what?" He asked.

"For sacrificing everything." She said quietly. Neo closed his eyes. All he could see was the dieing body of Trinity. He held her tight looking her straight in the eyes.

"I would do anything for you." He said truthfully. Trinity could feel tears building up in her eyes. She quickly wiped them away and laid her head on Neo's chest.

"I know." She said grateful for everything that had happened. Trinity, exhausted from the day, fell asleep right then and there. Neo fell asleep only minutes after her.

The next morning… 

Neo jolted awake when he heard someone knocking on the hard metal door. He carefully moved Trinity over so he could get up to answer the door. He successfully moved her without waking her so he walked over to the door and opened it quietly. He smiled when he saw that it was Morpheus.

"I'm sorry about waking you up but we will need to go soon." He said looking apologetic.

"Why?" Asked Neo.

"We got a message from the Oracle. She wants to talk to you as soon as possible." Said Morpheus catching Neo's interest.

"How soon can we leave?" He asked.

"As soon as you feel you can go." He said. Neo nodded. "I'll talk to Trinity about it."

"Sounds good." He said, "send me a messenger when you have agreed on a time."

"Okay." He said. Just before Morpheus turned to go back to his room, Trinity walked over.

"The Oracle?" She asked.

"Yes." Morpheus replied.

"When are we going to leave?" She asked.

"That, I am leaving up to Neo." Said Morpheus. Trinity looked at him.

"I don't care when we leave." Said Neo.

"How soon can we get the Neb ready to go?" Asked Trinity.

"A couple hours at most." Answered Morpheus. Neo could see what she was getting at.

"If we leave today, we can rest up on the Neb and then go see the Oracle in the morning." Neo said.

"Sounds good to me." Said Morpheus, "I'll alert Link."

"We'll start packing." Said Trinity. Morpheus nodded and left them to pack up.

"What does she want now?" Neo asked out loud.


	4. Author's Note

Author's Note

Hey everyone!! Hope your liking the story so far. I just need to write something about the next chapter. In the third movie (i say third because i can't bring my self to admit that Neo is dead) the Neb isn't even there. It was blown up in the second movie. so thy got a second one that looks extermely similar to it. well thats it. Keep readin and try to review it a bit more!!! bye!!!

(P.S. if you haden't noticed by now, it would help alot if you had seen all the movies before reading this.)

writing my hands off,

Sweetheartgrl13


	5. Chapter 4

Chapter 3

"Why now." Link moaned.

"Because Neo, Trinity and I are ready to go and we can't go without you." Reasoned Morpheus. Link sighed. He knew he was in a hole that he wouldn't be able to crawl out of.

"Fine. But Zee won't be very happy." He sighed. Morpheus smiled apologetically.

"Thank you Link." Morpheus said turning to leave. Link smiled a little and shut the door as Morpheus walked down the hall. Link sighed.

"Here we go again."

A couple hours and arguments later… 

Link walked up to the dock where the Neb was charging and saw that everyone was already there.

"Sorry I'm late. Zee had another fit about me leaving again." He said wincing.

"That's okay Link." Said Neo picking his bags up. Morpheus put in a code on the side of the ship so the back would open up so they could go in and start the ship. Trinity and Morpheus grabbed up their stuff and walked into the ship, Neo and Link followed. Neo and Trinity split off from Morpheus and Link to go put their bags in their rooms.

"It's funny how these things work." Rambled Trinity absent-mindedly. Neo looked up at her confused.

"How what things happen?" He asked. She looked up at him.

"Well, everything." She said stepping into her room. Neo stood in the doorway. "Everything that's happened so far. It's just too extreme." Neo nodded his head calmly.

"I know how you feel. I don't think that the other One's had it like I do." He joked, "But I'm glad that it's happening like it is."

"Why?" She asked walking out of her room and stopping right on front of him. Neo wrapped his arms around her and pulled her into a passionate kiss. A couple seconds later he pulled away.

"Because I have you." He said softly.

"That's a good enough reason for me." She said smiling.

"Hang on a second." Said Neo grabbing his bags and throwing them on his bed. He ran back out to Trinity and flung his arm around her.

"Let's go upstairs." Trinity said smiling. Morpheus and Link were already ready to go by the time they got up.

"Link, start the ship." Said Morpheus while doing a final check of the systems and supplies. Link nodded and started pumping the handle on the top of the control area. After pumping it a couple times he pushed a button on the bottom of the console and the ship buzzed to life. Link looked over to Morpheus.

"Do you mind if I go in back?" He asked.

"No, go ahead." He said pulling a headset on.

"Thanks." He said. Link got up and walked over to Neo and Trinity. "You guys want to train a bit."

"Yeah. Sounds good." Neo said. He looked at Trinity. "You want to go too?"

"Sure." She said enthusiastically.

Link sat down on the chair on front of the numerous screens. Three in the middle had a green code scrolling down the screen. He tapped one of the screens off to the right of the three middle screens and it flickered to life. The ones around it came on too. Link walked over to the chairs where Neo and Trinity were laying down, waiting to be plugged in.

"See you guys later." He said taking the metal rod behind Trinity off it's hook. Trinity looked over at Neo.

"I love you." She said smiling.

"I love you too." He said smiling back. Link rolled his eyes.

"You guys will only be a couple seconds apart." He said. Trinity laughed and rested her head on the back of the chair. Link smiled and plugged her in. Trinity's eyes closed less than a second later. Link walked over to Neo and plugged him in before going back over to the controls.

Neo opened his eyes and saw that he was in the usual white room with no end. The only contrast was Trinity in her sunglasses and usual outfit. Neo waked over to her and pulled off his sunglasses.

"I forgot how great you looked in that." She said smiling. Neo smiled back. He was about to say something when a ringing sound coming from his pocket interrupted him. Neo answered it reluctantly.

"Sorry to interrupt you guys but do you want to train or get a room?" He joked.

"Ha ha ha." Neo said sarcastically.

"What program do you want me to run?" He asked.

"The Dojo?" He suggested looking to Trinity. She shrugged. "Yeah the Dojo."

"Okay." He said. Neo could hear the clicking of a keyboard in the background. Suddenly the scenery changed to a Japanese Dojo. The first time he had been there it had been when he was first brought into the real world. Morpheus had fought him to test his abilities. He looked around and saw the same old familiar training facility that he was used to. He looked over at Trinity and smiled. They were both in their normal outfits and sunglasses.

"Don't worry." He said going in to the usual pre-fight pose. "I'll go easy on you."

"Don't." She said confidently. Neo beckoned to her smiling. "Bring it on."


	6. Chapter 5

Chapter 4

Neo and Trinity were completely still, both waiting for the other to move first. A huge grin spread over Neo's face while staring Trinity down. Suddenly Trinity crouched down and sprung at Neo like a cat faster than he blink. Neo dodged out of the way effortlessly and Trinity threw some punches only to be blocked every time. In a quick decision, Neo dropped to the ground and knocked Trinity's feet out from under her. Just before she hit the ground he caught her

"This will be very interesting." Trinity said smirking. She twirled out of Neo's arms going straight into a back flip. Neo slowly stood up, smiling back at Trinity. Neo gracefully ran to attack Trinity. Trinity, knowing she wouldn't be able to dodge him, faced him head on. Neo landed right on front of Trinity and pulled back his fist. Trinity braced herself but saw her chance when he hesitated. Trinity let loose a punch sending Neo stumbling backwards a couple of steps backwards.

"So that's how it's going to be." Laughed Neo catching his breath. Trinity smiled hoping she didn't hurt him that bad. Neo stood up and took a deep breath. Trinity quickly came up with a plan and watched diligently as Neo quickly recovered her attack. Neo took Trinity by surprise and attacked her when it looked like he was still recuperating. Trinity barely had anytime to react. If she hadn't been watching him she would be lying on her back on the ground right now.

Neo smiled when she dodged him. He landed softly on his feet and kept running. He ran straight up the wooden pole on the side of the room and back-flipped towards Trinity. Trinity remembered the last time he had done this trick and what happened too. Trinity positioned herself and prepared herself to do the unthinkable. Neo finished his flip and landed on front of Trinity. She was ready when he came down and kicked him square in the chest. Neo flew back and hit the wooden support behind him. He hit it so hard the support broke leaving Neo on the floor.

"Sorry." Trinity giggled. Neo got up immediately kicking himself for falling for that trick. Trinity gasped when she saw Neo charging at her with such speed. Trinity back-flipped away from him and ducked as he punched. Trinity found an opening in his attack and let loose a flurry of punches which Neo neatly blocked every time. Trinity was starting to get worried when she wasn't even getting through. Neo kept blocking her smugly. He saw she was starting to get a little tired so he turned the fight up a notch and kicked her all the way cross the room.

Trinity didn't know what hit her until she saw Neo was suddenly a lot farther away from her. Neo cautiously walked over to her as she stood up.

"You're going to get it now." She warned. Neo could see she wasn't kidding and he got a little worried. Trinity ran over to the front of the room and pulled a samurai sword off a rack.

"Oh shit." Neo muttered under his breath. Trinity unsheathed the sword and swung it around her a couple times getting used to the weight. Neo charged at her avoiding the sword as she swung it at him purposefully. Neo jumped behind her and grabbed a second sword off the rack and unsheathed it as fast as he could because Trinity was closing in on him rapidly. He got it off just in time to block the deadly blow that trinity had in store for him. The two exchanged blows for a minute, Neo always getting Trinity in the corners. Trinity caught a hit from Neo with his hands above his head so she made good use of his opening and kicked Neo in between the legs. Neo stumbled away.

"No fair." He groaned. Trinity laughed and stuck her sword in the floor. Neo leaned against one of the supports while Trinity hugged him.

"I'm sorry." She said giggling. Suddenly Neo grabbed her and wouldn't let her go.

"I didn't say pause did I?" He said while Trinity struggled to get out of his grip regretting her mistake.

"Come on." She wined, "Now that wasn't fair."

"Now were even." He laughed. Neo let go of her and did a roundhouse kick sending her stumbling back a couple steps. Neo started punching her repeatedly but softer than normal. He didn't want to kill her. Trinity sank to the floor when he stopped.

"You win." She gasped. Neo sat down next to her. He looked over at her and she looked at him. They both started laughing. Trinity leaned over and laid her head against Neo's shoulder. Neo wrapped his arm around her. Suddenly the scenery changed from the dojo to a beach at sunset. They both looked out to the brilliant colors of the setting sun. Neo looked down at Trinity and kissed her.

"Thank you link." In the Neb Link leaned back in his chair and smiled.

"My pleasure." He said getting up to go talk to Morpheus.


	7. Chapter 6

Chapter 0

Chapter 6

Morpheus guided the ship through the tunnel just outside the gates of Zion. Sentinels lined the walls but he wasn't worried. Part of the treaty was that the machines would help protect Zion. They weren't there to hurt them. Link walked into the cockpit and sat next to Morpheus.

"How are Neo and Trinity?" Asked Morpheus.

"They're resting right now." He said sitting down in the chair next to Morpheus, "I'll go down again in a minute." Morpheus nodded turning the ship down a tunnel and out of sight of the Sentinels. The two sat in silence for a minute. Finally Link got up and broke the silence.

"I'm going to go check on them." He said walking through the door. Link sat in his chair and called Neo. They were both where he had left them before.

Neo answered his phone reluctantly.

"Yeah?" Asked Neo.

"You guys need to get back in now. Were going up to broadcast depth." Link said.

"Okay." Neo said. He hung up and looked at Trinity.

"See you in a second." He said smiling. Trinity smiled back and disappeared right before his eyes. When Neo blinked again, he was back on the Nebuchadnezzar. Link unplugged Neo and Trinity and un-clasped their feet. Neo sat up and stretched. Trinity walked over and rested her elbow on his shoulder.

"Hungry?" She asked. Neo nodded and stood up. Trinity and Neo walked to the "dining room" and poured themselves some of the nutritious goop. They sat down next to each other and started eating.

"Nice job." Trinity said between bites.

"Thanks. You too." He said smiling. Trinity leaned her head against his shoulder. "But you do cheat a lot." She smiled.

"No one fights fair anymore." She said. Neo knew she had him there.

"How long till we get to the surface?" He asked Link who was pouring himself some of the goop too.

"Well if we don't run into any bad sentinels, a couple hours." He said sitting down. Neo nodded.

"I'm going to talk to Morpheus." Neo said standing up. Trinity smiled.

"I'll stay here." After all she didn't want to smother him. Link moved out of his was as he put his empty bowl away.

Morpheus was concentrating intensely as Neo walked in.

"Hello Neo." He said without looking up.

"Hi." Neo said sitting down in the chair next to him. The screen on front of him was light up with hundreds of eerie green dots, each dot representing a single sentinel. Morpheus looked on edge. The proximity alarm had been permanently turned off so they didn't know if the sentinels were good or bad. The only thing protecting the ship from the bad ones were the good ones guarding the ship and Neo. Neo was almost overwhelmed by all the sentinels surrounding them at first. He had learned to block them out unless he really needed to check up on things.

"We've had several close calls while you were sparing with Trinity." He stated. Neo wasn't surprised. Suddenly the screen light up with more green dots so that there was barely a single black spot left.

"Um Morpheus." Neo said still looking at the screen.

"What?" He said calmly.

"You should look at this." Neo said. Morpheus looked over and was speechless.

"Are they good or…"

"I don't know." Neo said. "This could be bad."

"Yes it could."


	8. Chapter 7

Chapter 0

Chapter 7

Neo watched the screen nervously as it turned more and more green every second. He could feel the tension in the air.

"Should I call Trinity and Link?" Neo asked.

"Yes." He said. "Tell them to go to the battle stations just in case.

"Okay." He replied walking over to the com on the wall. "Trinity?"

"Yes Neo?" she said after a few seconds.

"We have a situation. Sentinels are surrounding the ship but we don't know if they're good on not. We need you and link to head up to the battle stations right now. I'll do my thing in a minute here." Neo said.

"Okay. Just give us the word if you need us to shoot." Trinity said confidently.

"Okay thanks." He said before walking back over to the chair. "Anything new happen?"

"Well, if you look carefully at the screen, the sentinels are split into two groups. One group is surrounding us, the other surrounding them." Morpheus said while Neo studied the screen.

"Yeah I see what you mean." Neo said leaning back in the chair.

"Are you going to use your sight now?" Morpheus asked looking a little more relaxed.

"Yeah actually." He replied.

"Good. That will help us." He said quietly. Neo rested his hands on the chair and closed his eyes. Instead of seeing just black he saw bright lights all around him. The good sentinels were always a brighter glow that the bad ones. Neo searched through the crowd of lights but was very confused when he saw all the lights were exactly the same. Neo opened his eyes.

"They're all good." He said.

"What?" Morpheus asked as Neo walked over to the com again.

"Trinity?" He asked.

"Yes?" She replied.

"All the sentinels are good." He said.

"Really? Well that's good." She said.

"Yeah but why are they there?" He asked.

"I don't know." She said. "Maybe they're protecting us?"

"Maybe. But from what…"

"Shit Neo! Get over here!!"


	9. Another Authors Note

Hey everyone. I would just like to tell you all that my computer is not working any more so I need to buy a new one. I am currently keeping up to date on my reviews at the library and my grandma's house. I should have a new computer before the school year starts again (late August-early September) I appreciate your patience with me. I am going to post a new chapter for both of my fan fics asap. Thank you all for the reviews. I am glad that so many like my stories.

Sweetheartgrl13


	10. Good News From The Author

Hey every one! Good news! I got a computer now so I can start doing more fan fic!! I'm still doing this story and I'm going to start two new stories also! So im going to go now so I can start typing up the next chapters for your pleasure.

Sweetheartgrl13


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